Computational Investigation on the p53-MDM2 Interaction Using the Potential of Mean Force Study.

Abstract

Murine double minute 2 (MDM2) proteins are found to be overproduced by many human tumors in order to inhibit the functioning of p53 molecules, a tumor suppressor protein. Thus, reactivating p53 functioning in cancer cells by disrupting p53–MDM2 interactions may offer a significant approach in cancer treatment. However, the structural characterization of the p53–MDM2 complex at the atomistic level and the mechanism of binding/unbinding of the p53–MDM2 complex still remain unclear. Therefore, we demonstrate here the probable binding (unbinding) pathway of transactivation domain 1 of p53 during the formation (dissociation) of the p53–MDM2 complex in terms of free energy as a function of reaction coordinate from the potential of mean force (PMF) study using two different force fields: ff99SB and ff99SB-ILDN. From the PMF plot, we noticed the PMF to have a minimum value at a p53–MDM2 separation of 12 Å, with a dissociation energy of 30 kcal mol–1. We also analyzed the conformational dynamics and stability of p53 as a function of its distance of separation from MDM2. The secondary structure content (helix and turns) in p53 was found to vary with its distance of separation from MDM2. The p53–MDM2 complex structure with lowest potential energy was isolated from the ensemble at the reaction coordinate corresponding to the minimum PMF value and subjected to molecular dynamics simulation to identify the interface surface area, interacting residues at the interface, and the stability of the complex. The simulation results highlight the importance of hydrogen bonds and the salt bridge between Lys94 of MDM2 and Glu17 of p53 in the stability of the p53–MDM2 complex. We also carried out the binding free energy calculations and the per residue energy decomposition analyses of the interface residues of the p53–MDM2 complex. We found that the binding affinity between MDM2 and p53 is indeed high [ΔGbind = −7.29 kcal mol–1 from molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) and ΔGbind = −53.29 kcal mol–1 from molecular mechanics/generalized borne surface area]. The total binding energy obtained using the MM/PBSA method was noticed to be closer to the experimental values (−6.4 to −9.0 kcal mol–1). The p53–MDM2 complex binding profile was observed to follow the same trend even in the duplicate simulation run and also in the simulation carried out with different force fields. We found that Lys51, Leu54, Tyr100, and Tyr104 from MDM2 and the residues Phe19, Trp23, and Leu26 from p53 provide the highest energy contributions for the p53–MDM2 interaction. Our findings highlight the prominent structural and binding characteristics of the p53–MDM2 complex that may be useful in designing potential inhibitors to disrupt the p53–MDM2 interactions.